Iterative linearized density matrix propagation for modeling coherent excitation energy transfer in photosynthetic light harvesting

Journal of Chemical Physics

Volumn 133, Issue 18, 2010, Pages

  Huo, P ^a   Coker, D F ^a,b  

^a Boston University ^*  (United States)

^b UNIVERSITY COLLEGE DUBLIN   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

COHERENT EXCITATIONS; COHERENT SUPERPOSITION STATE; DECOHERENCE; DEGREES OF FREEDOM; DENSITY MATRIX; DISCRETE PATH; EXCITON TRANSFER; EXCITONIC SYSTEMS; EXPERIMENTAL EVIDENCE; GENERAL DESCRIPTION; GREEN SULFUR BACTERIA; LIGHT HARVESTING COMPLEXES; LIGHT-HARVESTING SYSTEMS; MARKOVIAN APPROXIMATION; NONPERTURBATIVE; PERTURBATIVE APPROACH; PHOTOSYNTHETIC LIGHT; SHORT TIME APPROXIMATION;

BACTERIA; CHROMOPHORES; ENERGY TRANSFER; EXCITATION ENERGY; HARVESTING; LINEARIZATION; QUANTUM THEORY; SULFUR;

ENERGY HARVESTING;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; CHLOROBI; ENERGY TRANSFER; MOLECULAR DYNAMICS; MONTE CARLO METHOD; PHOTOSYNTHESIS; PROBABILITY; QUANTUM THEORY;

CHLOROBI; ENERGY TRANSFER; MARKOV CHAINS; MODELS, CHEMICAL; MOLECULAR DYNAMICS SIMULATION; MONTE CARLO METHOD; PHOTOSYNTHETIC REACTION CENTER COMPLEX PROTEINS; QUANTUM THEORY;

EID: 78449295531     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3498901     Document Type: Article

References (70)

1. A. Damjanovic, F. Autenrieth, X. Hu, T. Ritz, and K. Schulten, Q. Rev. Biophys. QURBAW 0033-5835 35, 1 (2002).
2. G. D. Scholes, Annu. Rev. Phys. Chem. ARPLAP 0066-426X 54, 57 (2003). 10.1146/annurev.physchem.54.011002.103746
3. R. E. Fenna and B. W. Matthews, Nature (London) NATUAS 0028-0836 258, 573 (1975). 10.1038/258573a0
4. A. Camara-Artigas, R. E. Blankenship, and J. P. Allen, Photosynth. Res. PHRSDI 0166-8595 75, 49 (2003). 10.1023/A:1022406703110 (Pubitemid 36333176)
5. J. L. Herek, N. J. Fraser, T. Pullerits, P. Martinsson, T. Polivka, H. Scheer, R. J. Cogdell, and V. Sundstrom, Biophys. J. BIOJAU 0006-3495 78, 2590 (2000). 10.1016/S0006-3495(00)76803-2
6. M. A. Thompson, M. C. Zerner, and J. Fajer, J. Phys. Chem. JPCHAX 0022-3654 95, 5693 (1991). 10.1021/j100167a058
7. J. A. Leegwater, Prog. Biophys. Mol. Biol. PBIMAC 0079-6107 65, PE204 (1996).
8. Y. F. Li, W. L. Zhou, R. E. Blankenship, and J. P. Allen, J. Mol. Biol. JMOBAK 0022-2836 271, 456 (1997). 10.1006/jmbi.1997.1189 (Pubitemid 27348510)
9. N. Makri, E. J. Sim, D. E. Makarov, and M. Topaler, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 93, 3926 (1996). 10.1073/pnas.93.9.3926 (Pubitemid 26144224)
10. E. Sim and N. Makri, J. Phys. Chem. B JPCBFK 1089-5647 101, 5446 (1997). 10.1021/jp970707g
11. S. Savikhin, D. R. Buck, and W. S. Struve, Chem. Phys. CMPHC2 0301-0104 223, 303 (1997). 10.1016/S0301-0104(97)00223-1 (Pubitemid 128001699)
12. G. S. Engel, T. R. Calhoun, E. L. Read, T. -K. Ahn, T. Mancal, Y. -C. Cheng, R. E. Blankenship, and G. R. Fleming, Nature (London) NATUAS 0028-0836 446, 782 (2007). 10.1038/nature05678 (Pubitemid 46582029)
13. H. Lee, Y. -C. Cheng, and G. R. Fleming, Science SCIEAS 0036-8075 316, 1462 (2007). 10.1126/science.1142188 (Pubitemid 46906609)
14. A. Ishizaki and G. R. Fleming, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 106, 17255 (2009). 10.1073/pnas.0908989106
15. E. Collini, C. Y. Wong, K. E. Wilk, P. M. G. Curmi, P. Brumer, and G. D. Scholes, Nature NATUAS 0028-0836 463, 644 (2010). 10.1038/nature08811
16. G. D. Scholes, J. Phys. Chem. Lett. 1, 2 (2010). 10.1021/jz900062f
17. S. Jang, M. D. Newton, and R. J. Silbey, Phys. Rev. Lett. PRLTAO 0031-9007 92, 218301 (2004). 10.1103/PhysRevLett.92.218301
18. S. Jang, M. D. Netwton, and R. J. Silbey, J. Phys. Chem. B JPCBFK 1089-5647 111, 6807 (2007). 10.1021/jp070111l
19. Y. -C. Cheng and R. J. Silbey, Phys. Rev. Lett. PRLTAO 0031-9007 96, 028103 (2006). 10.1103/PhysRevLett.96.028103 (Pubitemid 43248297)
20. C. P. Hsu, G. R. Fleming, M. Head-Gordon, and T. Head-Gordon, J. Chem. Phys. JCPSA6 0021-9606 114, 3065 (2001). 10.1063/1.1338531 (Pubitemid 32253426)
21. R. Ḿtivier, F. Nolde, K. Muellen, and T. Basch́, Phys. Rev. Lett. PRLTAO 0031-9007 98, 047802 (2007). 10.1103/PhysRevLett.98.047802 (Pubitemid 46168670)
22. D. J. Heijs, V. A. Malyshev, and J. Knoester, Phys. Rev. Lett. PRLTAO 0031-9007 95, 177402 (2005). 10.1103/PhysRevLett.95.177402 (Pubitemid 41777393)
23. M. Schröder, U. Kleinekathofer, and M. Schreiber, J. Chem. Phys. JCPSA6 0021-9606 124, 084903 (2006). 10.1063/1.2171188
24. S. Jang, J. Chem. Phys. JCPSA6 0021-9606 127, 174710 (2007). 10.1063/1.2779031 (Pubitemid 350075546)
25. S. Jang, M. D. Newton, and R. J. Silbey, J. Chem. Phys. JCPSA6 0021-9606 118, 9312 (2003). 10.1063/1.1569239
26. S. Jang and R. J. Silbey, J. Chem. Phys. JCPSA6 0021-9606 118, 9324 (2003). 10.1063/1.1569240
27. A. Olaya-Castro, C. Fan-Lee, F. Fassioli-Olsen, and N. F. Johnson, Phys. Rev. B PLRBAQ 0556-2805 78, 085115 (2008). 10.1103/PhysRevB.78.085115
28. X. J. Yang, T. E. Dykstra, and G. D. Scholes, Phys. Rev. B PLRBAQ 0556-2805 71, 045203 (2005). 10.1103/PhysRevB.71.045203 (Pubitemid 40418078)
29. M. N. Yang, J. Chem. Phys. JCPSA6 0021-9606 123, 124705 (2005). 10.1063/1.2046668 (Pubitemid 41407802)
30. B. Palmieri, D. Abramavicius, and S. Mukamel, J. Chem. Phys. JCPSA6 0021-9606 130, 204512 (2009). 10.1063/1.3142485
31. A. Ishizaki and G. R. Fleming, J. Chem. Phys. JCPSA6 0021-9606 130, 234110 (2009). 10.1063/1.3155214
32. A. Ishizaki and G. R. Fleming, J. Chem. Phys. JCPSA6 0021-9606 130, 234111 (2009). 10.1063/1.3155372
33. P. Rebentrost, R. Chakraborty, and A. Aspuru-Guzik, J. Chem. Phys. JCPSA6 0021-9606 131, 184102 (2009). 10.1063/1.3236844
34. J. Piilo, S. Maniscalco, K. Häkönen, and K. -A. Suominen, Phys. Rev. Lett. PRLTAO 0031-9007 100, 180402 (2008). 10.1103/PhysRevLett.100.180402 (Pubitemid 351654659)
35. J. Piilo, K. Häkönen, S. Maniscalco, and K. -A. Suominen, Phys. Rev. A PLRAAN 1050-2947 79, 062112 (2009). 10.1103/PhysRevA.79.062112
36. S. Jang, Y. -C. Cheng, D. R. Reichman, and J. D. Eaves, J. Chem. Phys. JCPSA6 0021-9606 129, 101104 (2008). 10.1063/1.2977974
37. S. Jang, J. Chem. Phys. JCPSA6 0021-9606 131, 164101 (2009). 10.1063/1.3247899
38. G. Tao and W. H. Miller, J. Phys. Chem. Lett. 1, 891 (2010). 10.1021/jz1000825
39. H. -D. Meyer and W. H. Miller, J. Chem. Phys. JCPSA6 0021-9606 70, 3214 (1979). 10.1063/1.437910
40. G. Stock and M. Thoss, Phys. Rev. Lett. PRLTAO 0031-9007 78, 578 (1997). 10.1103/PhysRevLett.78.578
41. X. Sun and W. H. Miller, J. Chem. Phys. JCPSA6 0021-9606 106, 6346 (1997). 10.1063/1.473624
42. M. Thoss and G. Stock, Phys. Rev. A PLRAAN 1050-2947 59, 64 (1999). 10.1103/PhysRevA.59.64
43. E. R. Dunkel, S. Bonella, and D. F. Coker, J. Chem. Phys. JCPSA6 0021-9606 129, 114106 (2008). 10.1063/1.2976441
44. S. Bonella and D. F. Coker, J. Chem. Phys. JCPSA6 0021-9606 122, 194102 (2005). 10.1063/1.1896948 (Pubitemid 40914299)
45. S. Bonella and D. F. Coker, J. Chem. Phys. JCPSA6 0021-9606 118, 4370 (2003). 10.1063/1.1542883
46. S. Bonella and D. F. Coker, J. Chem. Phys. JCPSA6 0021-9606 114, 7778 (2001). 10.1063/1.1366331 (Pubitemid 32486691)
47. P. Huo, S. Bonella, L. Chen, and D. F. Coker, Chem. Phys. CMPHC2 0301-0104 370, 87 (2010). 10.1016/j.chemphys.2010.02.021
48. R. Hernandez and G. A. Voth, Chem. Phys. CMPHC2 0301-0104 233, 243 (1998). 10.1016/S0301-0104(98)00027-5 (Pubitemid 128111762)
49. J. A. Poulsen, G. Nyman, and P. J. Rossky, J. Chem. Phys. JCPSA6 0021-9606 119, 12179 (2003). 10.1063/1.1626631
50. Q. Shi and E. Geva, J. Phys. Chem. A JPCAFH 1089-5639 107, 9059 (2003). 10.1021/jp030497+
51. H. Wang, X. Sun, and W. H. Miller, J. Chem. Phys. JCPSA6 0021-9606 108, 9726 (1998). 10.1063/1.476447
52. M. F. Herman and D. F. Coker, J. Chem. Phys. JCPSA6 0021-9606 111, 1801 (1999). 10.1063/1.479449
53. Z. Ma and D. F. Coker, J. Chem. Phys. JCPSA6 0021-9606 128, 244108 (2008). 10.1063/1.2944270
54. M. Sarovar, A. Ishizaki, G. R. Fleming, and K. B. Whaley, Nat. Phys. ZZZZZZ 1745-2473 6, 462 (2010). 10.1038/nphys1652
55. J. Adolphs and T. Renger, Biophys. J. BIOJAU 0006-3495 91, 2778 (2006). 10.1529/biophysj.105.079483 (Pubitemid 44526469)
56. M. Cho, H. M. Vaswani, T. Brixner, J. Stenger, and G. R. Fleming, J. Phys. Chem. B JPCBFK 1089-5647 109, 10542 (2005). 10.1021/jp050788d (Pubitemid 40844481)
57. R. J. W. Louwe, J. Vrieze, A. J. Hoff, and T. J. Aartsma, J. Phys. Chem. B JPCBFK 1089-5647 101, 11280 (1997). 10.1021/jp9722162
58. T. Renger and V. May, J. Phys. Chem. A JPCAFH 1089-5639 102, 4381 (1998). 10.1021/jp9800665
59. S. I. E. Vulto, M. A. de Baat, R. J. W. Louwe, H. P. Permentier, T. Neef, M. Miller, H. van Amerongen, and T. J. Aartsma, J. Phys. Chem. B JPCBFK 1089-5647 102, 9577 (1998). 10.1021/jp982095l
60. M. Wendling, M. A. Przyjalgowski, D. Gülen, S. I. E. Vulto, T. J. Aartsma, R. van Grondelle, and H. van Amerongen, Photosynth. Res. PHRSDI 0166-8595 71, 99 (2002). 10.1023/A:1014947732165 (Pubitemid 34416080)
61. Y. C. Cheng and R. J. Silbey, J. Phys. Chem. B JPCBFK 1089-5647 109, 21399 (2005). 10.1021/jp051303o (Pubitemid 41698314)
62. N. Makri, J. Phys. Chem. B JPCBFK 1089-5647 103, 2823 (1999). 10.1021/jp9847540
63. H. Wang, M. Thoss, K. L. Sorge, R. Gelabert, X. Giḿnez, and W. H. Miller, J. Chem. Phys. JCPSA6 0021-9606 114, 2526 (2001).
64. D. Mac Kernan, G. Ciccotti, and R. Kapral, J. Chem. Phys. JCPSA6 0021-9606 116, 2346 (2002). 10.1063/1.1433502 (Pubitemid 34167969)
65. O. V. Prezhdo and P. J. Rossky, J. Chem. Phys. JCPSA6 0021-9606 107, 5863 (1997). 10.1063/1.474312
66. O. V. Prezhdo and P. J. Rossky, Phys. Rev. Lett. PRLTAO 0031-9007 81, 5294 (1998). 10.1103/PhysRevLett.81.5294
67. K. H. Hughes, C. D. Christ, and I. Burghardt, J. Chem. Phys. JCPSA6 0021-9606 131, 024109 (2009). 10.1063/1.3159671
68. D. F. Coker, L. Chen, P. Huo, and S. Bonella, in Multidimensional Quantum Mechanics with Trajectories, edited by, D. Shalashilin, and, M. P. de Miranda, (CCP6, Daresbury, 2008), p. 165.
69. M. S. Causo, G. Ciccotti, D. Montemayor, S. Bonella, and D. F. Coker, J. Phys. Chem. B JPCBFK 1089-5647 109, 6855 (2005). 10.1021/jp045208b (Pubitemid 40538455)
70. S. Bonella and D. F. Coker, in Quantum Dynamics of Complex Molecular Systems, Lectures in Chemical Physics Vol. 83, edited by, D. Micha, and, I. Burghardt, (Springer, Berlin, 2006), p. 321.